tools:::Rd_package_description("dae")
Version: utils::packageDescription("dae", fields="Version")
Date: utils::packageDescription("dae", fields="Date")
| (i) Data | |
ABC.Interact.dat | Randomly generated set of values indexed by |
| three factors | |
BIBDWheat.dat | Data for a balanced incomplete block experiment |
Casuarina.dat | Data for an experiment with rows and columns from |
| Williams (2002) | |
Exp249.munit.des | Systematic, main-plot design for an experiment to be |
| run in a greenhouse | |
Fac4Proc.dat | Data for a 2^4 factorial experiment |
LatticeSquare_t49.des | A Lattice square design for 49 treatments |
McIntyreTMV.dat | The design and data from McIntyre (1955) two-phase |
| experiment | |
Oats.dat | Data for an experiment to investigate nitrogen response |
| of 3 oats varieties | |
Sensory3Phase.dat | Data for the three-phahse sensory evaluation |
| experiment in Brien, C.J. and Payne, R.W. (1999) | |
Sensory3PhaseShort.dat | Data for the three-phase sensory evaluation |
| experiment in Brien, C.J. and Payne, R.W. (1999), | |
| but with short factor names | |
SPLGrass.dat | Data for an experiment to investigate the |
| effects of grazing patterns on pasture | |
| composition | |
| (ii) Factor manipulation functions | |
| Forms a new or revised factor: | |
fac.combine | |
| Combines several factors into one | fac.nested |
| Creates a factor, the nested factor, whose values are | |
| generated within those of a nesting factor | fac.recast |
| Recasts a factor by modifying the values in the factor vector | |
| and/or the levels attribute, possibly combining | |
| some levels into a single level. | fac.recode |
| Recodes factor 'levels' using possibly nonunique | |
| values in a vector. (May be deprecated in future.) | fac.uselogical |
| Forms a two-level factor from a logical object | |
| Forms multiple new factors: | |
fac.divide | Divides a factor into several separate factors |
fac.gen | Generate all combinations of several factors and, |
| optionally, replicate them | |
fac.genfactors | Generate all combinations of the levels of the supplied |
| factors, without replication | |
fac.multinested | Creates several factors, one for each level of the nesting factor |
| and each of whose values are either generated within those of | |
| a level of the nesting factor or using the values of the nested | |
| factor within the levels of the nesting factor. | |
fac.split | Splits a factor whose levels consist of several delimited |
| strings into several factors. | |
fac.uncombine | Cleaves a single factor, each of whose levels has delimited |
| strings, into several factors using the separated strings. | |
| Operates on factors: | |
as.numfac | |
| Convert a factor to a numeric vector, possibly centering or | |
| scaling the values | mpone |
| Converts the first two levels of a factor into | |
| the numeric values -1 and +1 | fac.match |
| Match, for each combination of a set of columns | |
| in 'x', the row that has the same combination | |
| in 'table' | |
| (iii) Design functions | |
| Designing experiments: | |
designLatinSqrSys | Generate a systematic plan for a Latin Square design. |
designRandomize | Randomize allocated to recipient factors to produce |
a layout for an experiment. It supersedes fac.layout. | |
no.reps | Computes the number of replicates for an experiment |
detect.diff | Computes the detectable difference for an experiment |
power.exp | Computes the power for an experiment |
| Plotting designs: | |
blockboundaryPlot | |
| This function plots a block boundary on a plot | |
| produced by 'designPlot'. It supersedes | |
| blockboundary.plot. | designBlocksGGPlot |
Adds block boundaries to a plot produced by designGGPlot. | designGGPlot |
| Plots labels on a two-way grid of coloured cells using ggplot2 | |
| to represent an experimental design. | designPlot |
| A graphical representation of an experimental design | |
| using labels stored in a matrix. | |
| It superseded design.plot. | designPlotlabels |
| Plots labels on a two-way grid using ggplot2. | |
| Assessing designs: | |
designAmeasures | Calculates the A-optimality measures from the |
| variance matrix for predictions. | |
designAnatomy | Given the layout for a design, obtain its anatomy via |
| the canonical analysis of its projectors to show the | |
| confounding and aliasing inherent in the design. | |
designTwophaseAnatomies | Given the layout for a design and three structure formulae, |
| obtain the anatomies for the (i) two-phase, | |
| (ii) first-phase, (iii) cross-phase, treatments, and | |
| (iv) combined-units designs. | |
marginality.pstructure | Extracts the marginality matrix from a |
pstructure.object | |
marginality.pstructure | Extracts a list containing the marginality matrices from |
a pcanon.object | |
print.aliasing | Prints an aliasing data.frame |
summary.pcanon | Summarizes the anatomy of a design, being the |
| decomposition of the sample space based on its | |
| canonical analysis. | |
| (iv) ANOVA functions | |
fitted.aovlist | |
| Extract the fitted values for a fitted model | |
| from an aovlist object | fitted.errors |
| Extract the fitted values for a fitted model | interaction.ABC.plot |
| Plots an interaction plot for three factors | qqyeffects |
| Half or full normal plot of Yates effects | resid.errors |
| Extract the residuals for a fitted model | residuals.aovlist |
| Extract the residuals from an aovlist object | strength |
| Generate paper strength values | tukey.1df |
| Performs Tukey's | |
| one-degree-of-freedom-test-for-nonadditivity | yates.effects |
| Extract Yates effects | |
| (v) Matrix functions | |
| Operates on matrices: | |
elements | Extract the elements of an array specified by |
| the subscripts | |
mat.dirprod | Forms the direct product of two matrices |
mat.dirsum | Forms the direct sum of a list of matrices |
mat.ginv | Computes the generalized inverse of a matrix |
Zncsspline | Forms the design matrix for fitting the |
| random effects for a natural cubic smoothing | |
| spline. | |
| Compute variance matrices for | |
| supplied variance component values: | |
mat.random | Calculates the variance matrix for the |
| random effects from a mixed model, based | |
| on a formula or a supplied matrix | |
mat.Vpred | Forms the variance matrix of predictions |
| based on supplied matrices | |
mat.Vpredicts | Forms the variance matrix of predictions, |
| based on supplied matrices or formulae. | |
| Forms matrices using factors | |
| stored in a data.frame: | |
fac.ar1mat | Forms the ar1 correlation matrix for a |
| (generalized) factor | |
fac.sumop | Computes the summation matrix that produces |
| sums corresponding to a (generalized) factor | |
fac.vcmat | Forms the variance matrix for the variance |
| component of a (generalized) factor | |
| Forms patterned matrices: | |
mat.I | |
| Forms a unit matrix | mat.J |
| Forms a square matrix of ones | mat.ncssvar |
| Forms a variance matrix for random cubic | |
| smoothing spline effects | |
| Forms correlation matrices: | |
mat.cor | Forms a correlation matrix in which all |
| correlations have the same value | |
mat.corg | Forms a general correlation matrix in which |
| all correlations have different values | |
mat.ar1 | Forms an ar1 correlation matrix |
mat.ar2 | Forms an ar2 correlation matrix |
mat.ar3 | Forms an ar3 correlation matrix |
mat.arma | Forms an arma correlation matrix |
mat.banded | Forms a banded matrix |
mat.exp | Forms an exponential correlation matrix |
mat.gau | Forms a gaussian correlation matrix |
mat.ma1 | Forms an ma1 correlation matrix |
mat.ma2 | Forms an ma2 correlation matrix |
mat.sar | Forms an sar correlation matrix |
mat.sar2 | Forms an sar2 correlation matrix |
| (vi) Projector and canonical efficiency functions | |
| Projector class: | |
projector | Create projectors |
projector-class | Class projector |
is.projector | Tests whether an object is a valid object of |
| class projector | |
print.projector | Print projectors |
correct.degfree | Check the degrees of freedom in an object of |
| class projector | |
degfree | Degrees of freedom extraction and replacement |
| Accepts two or more formulae: | |
designAnatomy | |
| An anatomy of a design, obtained from | |
| a canonical analysis of the relationships | |
| between sets of projectors. | summary.pcanon |
| Summarizes the anatomy of a design, being the | |
| decomposition of the sample space based on its | |
| canonical analysis | print.summary.pcanon |
| Prints the values in an 'summary.pcanon' object | efficiencies.pcanon |
| Extracts the canonical efficiency factors from a | |
| list of class 'pcanon' | |
| Accepts exactly two formulae: | |
projs.2canon | A canonical analysis of the relationships between |
| two sets of projectors | |
projs.combine.p2canon | Extract, from a p2canon object, the projectors |
summary.p2canon | A summary of the results of an analysis of |
| the relationships between two sets of projectors | |
print.summary.p2canon | Prints the values in an 'summary.p2canon' object |
| that give the combined decomposition | |
efficiencies.p2canon | Extracts the canonical efficiency factors from |
| a list of class 'p2canon' | |
| Accepts a single formula: | |
as.data.frame.pstructure | |
| Coerces a pstructure.object to a data.frame | print.pstructure |
| Prints a pstructure.object | pstructure.formula |
| Takes a formula and constructs a pstructure.object | |
| that includes the orthogonalized projectors for the | |
| terms in a formula | porthogonalize.list |
Takes a list of projectors and constructs | |
a pstructure.object that includes projectors, | |
| each of which has been orthogonalized to all projectors | |
| preceding it in the list. | Others: |
decomp.relate | |
| Examines the relationship between the | |
| eigenvectors for two decompositions | efficiency.criteria |
| Computes efficiency criteria from a set of | |
| efficiency factors | fac.meanop |
| Computes the projection matrix that produces means | proj2.eigen |
| Canonical efficiency factors and eigenvectors | |
| in joint decomposition of two projectors | proj2.efficiency |
| Computes the canonical efficiency factors for | |
| the joint decomposition of two projectors | proj2.combine |
| Compute the projection and Residual operators | |
| for two, possibly nonorthogonal, projectors | show-methods |
| Methods for Function 'show' in Package dae | |
| (vii) Miscellaneous functions | |
extab | Expands the values in table to a vector |
get.daeRNGkind | Gets the value of daeRNGkind for the package dae from |
| the daeEnv environment. | |
get.daeTolerance | Gets the value of daeTolerance for the package dae. |
harmonic.mean | Calcuates the harmonic mean. |
is.allzero | Tests whether all elements are approximately zero |
rep.data.frame | Replicate the rows of a data.frame by repeating |
| each row consecutively and/or repeating all rows | |
| as a group. | |
rmvnorm | Generates a vector of random values from a |
| multivariate normal distribution | |
set.daeRNGkind | Sets the values of daeRNGkind for the package dae in |
| the daeEnv environment' | |
set.daeTolerance | Sets the value of daeTolerance for the package dae. |
tools:::Rd_package_author("dae")
Maintainer: tools:::Rd_package_maintainer("dae")